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Urbanization is commonly associated with biodiversity loss and habitat fragmentation. However, urban environments often have greenspaces that can support wildlife populations, including rare species. The challenge for conservation planners working in these systems is identifying priority habitats and corridors for protection before they are lost. In a rapidly changing urban environment, this requires prompt decisions informed by accurate spatial information. Here, we combine several approaches to map habitat and assess connectivity for a diverse set of rare species in seven urban study areas across southern Michigan, USA. We incorporated multiple connectivity tools for a comprehensive appraisal of species‐habitat patterns across these urban landscapes. We observed distinct differences in connectivity by taxonomic group and site. The three turtle species (Blanding's, Eastern Box, and Spotted) consistently had more habitat predicted to be suitable per site than other evaluated species. This is promising for this at‐risk taxonomic group and allows conservation efforts to focus on mitigating threats such as road mortality. Grassland and prairie‐associated species (American Bumble Bee, Black and Gold Bumble Bee, and Henslow's Sparrow) had the least amount of habitat on a site‐by‐site basis. Kalamazoo and the northern Detroit sites had the highest levels of multi‐species connectivity across the entire study area based on the least cost paths. These connectivity results have direct applications in urban planning. Kalamazoo, one of the focal urban regions, has implemented a Natural Features Protection (NFP) plan to bolster natural area protections within the city. We compared our connectivity results to the NFP area and show where this plan will have an immediate positive impact and additional areas for potential consideration in future expansions of the protection network. Our results show that conservation opportunities exist within each of the assessed urban areas for maintaining rare species, a key benefit of this multi‐species and multi‐site approach. [ABSTRACT FROM AUTHOR]